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- PDB-5ht8: Crystal structure of clostrillin double mutant (S17H,S19H) in com... -

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Basic information

Entry
Database: PDB / ID: 5ht8
TitleCrystal structure of clostrillin double mutant (S17H,S19H) in complex with nickel
ComponentsBeta and gamma crystallin
KeywordsMETAL BINDING PROTEIN / Mutant of a betagamma-crystallin domain / Clostridium beijerinckii / Nickel bound form
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Beta-1,3-glucanase, N-terminal, subdomain 2 / Glycosyl hydrolases family 64 (GH64) domain profile. / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / : / CBM56 (carbohydrate binding type-56) domain profile. / Crystallins / Gamma-B Crystallin; domain 1 / Crystallins beta and gamma 'Greek key' motif profile. ...Beta-1,3-glucanase, N-terminal, subdomain 2 / Glycosyl hydrolases family 64 (GH64) domain profile. / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / : / CBM56 (carbohydrate binding type-56) domain profile. / Crystallins / Gamma-B Crystallin; domain 1 / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Beta and gamma crystallin
Similarity search - Component
Biological speciesClostridium beijerinckii NCIMB 8052 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsJamkhindikar, A. / Srivastava, S.S. / Sankaranarayanan, R.
CitationJournal: Biochemistry / Year: 2017
Title: A Transition Metal-Binding, Trimeric beta gamma-Crystallin from Methane-Producing Thermophilic Archaea, Methanosaeta thermophila
Authors: Srivastava, S.S. / Jamkhindikar, A.A. / Raman, R. / Jobby, M.K. / Chadalawada, S. / Sankaranarayanan, R. / Sharma, Y.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta and gamma crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8542
Polymers10,7961
Non-polymers591
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area4440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.687, 77.687, 74.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-225-

HOH

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Components

#1: Protein Beta and gamma crystallin


Mass: 10795.767 Da / Num. of mol.: 1 / Fragment: UNP residues 118-213 / Mutation: S17H,S19H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii NCIMB 8052 (bacteria)
Strain: NCIMB 8052 / Gene: Cbei_2825 / Plasmid: PET21A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6LX94
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.0M Ammonium Sulfate, 0.1M Bis-Tris, 5mM NiCl2 / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 14, 2015
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.01→25 Å / Num. obs: 7877 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 25.25 Å2 / Rmerge(I) obs: 0.125 / Χ2: 1.448 / Net I/av σ(I): 16.654 / Net I/σ(I): 15.5 / Num. measured all: 63993
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.01-2.086.80.4497551.21998.8
2.08-2.178.20.3477621.38299.9
2.17-2.2680.3337631.277100
2.26-2.388.50.2997841.344100
2.38-2.538.50.2587721.353100
2.53-2.738.30.2257911.268100
2.73-38.50.1697871.531100
3-3.438.30.1217901.448100
3.43-4.328.20.0858081.72899.9
4.32-2580.0658651.83100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.01 Å24.57 Å
Translation2.01 Å24.57 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IAJ

3iaj


Resolution: 2.01→24.567 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 545 6.92 %Random selection
Rwork0.1995 7329 --
obs0.202 7874 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.13 Å2 / Biso mean: 28.4573 Å2 / Biso min: 17.44 Å2
Refinement stepCycle: final / Resolution: 2.01→24.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms693 0 1 42 736
Biso mean--41.8 33.75 -
Num. residues----87
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007714
X-RAY DIFFRACTIONf_angle_d0.929979
X-RAY DIFFRACTIONf_chiral_restr0.04107
X-RAY DIFFRACTIONf_plane_restr0.004123
X-RAY DIFFRACTIONf_dihedral_angle_d11.687243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0102-2.21240.25331200.2021798X-RAY DIFFRACTION100
2.2124-2.53220.22231440.19981772X-RAY DIFFRACTION100
2.5322-3.18930.25711170.21811856X-RAY DIFFRACTION100

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